How to download KEGG pathways for list of enriched genes
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Wuschel ▴ 10
@wuschel-15944
Last seen 5 weeks ago
HUJI

I have a set of the interested gene list (Arabidopsis. TAIR IDs)

I want to find where these genes are enriched in KEGG pathways.

How can I do this not using online web tools?

How can I download KEGG pathways for the Arabidopsis genome in a CSV file? So later I can use R to work manually.

RNASeqRData GO • 101 views
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@gordon-smyth
Last seen 1 hour ago
WEHI, Melbourne, Australia

Arabidopsis thaliana:

library(limma)
ath.kegg <- getGeneKEGGLinks(species.KEGG = "ath")
head(ath.kegg)

Arabidopsis lyrata:

aly.kegg <- getGeneKEGGLinks(species.KEGG = "aly")

The resulting data.frames can be input to kegga to do an enrichment analysis for a set of DE genes.

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Thank you very much, Prof. appreciates it.

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